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Bayesian Analysis with Python

Unleash the power and flexibility of the Bayesian

framework

Osvaldo Martin

BIRMINGHAM - MUMBAI
Bayesian Analysis with Python

Copyright © 2016 Packt Publishing

All rights reserved. No part of this book may be reproduced, stored in a retrieval
system, or transmitted in any form or by any means, without the prior written
permission of the publisher, except in the case of brief quotations embedded in
critical articles or reviews.

Every effort has been made in the preparation of this book to ensure the accuracy
of the information presented. However, the information contained in this book
is sold without warranty, either express or implied. Neither the author nor Packt
Publishing, and its dealers and distributors will be held liable for any damages
caused or alleged to be caused directly or indirectly by this book.

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However, Packt Publishing cannot guarantee the accuracy of this information.

First published: November 2016

Production reference: 1211116

Published by Packt Publishing Ltd.

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Birmingham B3 2PB, UK.

ISBN 978-1-78588-380-4
www.packtpub.com
 Credits

Author Project Coordinator

Osvaldo Martin Nidhi Joshi

Reviewer Proofreader
Austin Rochford Safis Editor

Commissioning Editor Indexer

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Acquisition Editor Graphics

Tushar Gupta Disha Haria

Content Development Editor Production Coordinator

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Safis Editing
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 About the Author

Osvaldo Martin is a researcher at The National Scientific and Technical Research

Council (CONICET), the main organization in charge of the promotion of science
and technology in Argentina. He has worked on structural bioinformatics and
computational biology problems, especially on how to validate structural protein
models. He has experience in using Markov Chain Monte Carlo methods to simulate
molecules and loves to use Python to solve data analysis problems. He has taught
courses about structural bioinformatics, Python programming, and, more recently,
Bayesian data analysis. Python and Bayesian statistics have transformed the way he
looks at science and thinks about problems in general. Osvaldo was really motivated
to write this book to help others in developing probabilistic models with Python,
regardless of their mathematical background. He is an active member of the PyMOL
community (a C/Python-based molecular viewer), and recently he has been making
small contributions to the probabilistic programming library PyMC3.

I would like to thank my wife, Romina, for her support while writing
this book and in general for her support in all my projects, specially
the unreasonable ones. I also want to thank Walter Lapadula,
Juan Manuel Alonso, and Romina Torres-Astorga for providing
invaluable feedback and suggestions on my drafts.
A special thanks goes to the core developers of PyMC3. This book
was possible only because of the dedication, love, and hard work
they have put into PyMC3. I hope this book contributes to the spread
and adoption of this great library.
 About the Reviewer

Austin Rochford is a principal data scientist at Monetate Labs, where he

develops products that allow retailers to personalize their marketing across billions
of events a year. He is a mathematician by training and is a passionate advocate of
Bayesian methods.
 www.PacktPub.com

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 Table of Contents
Preface vii
Chapter 1: Thinking Probabilistically - A Bayesian Inference Primer 1
Statistics as a form of modeling 2
Exploratory data analysis 2
Inferential statistics 3
Probabilities and uncertainty 5
Probability distributions 7
Bayes' theorem and statistical inference 10
Single parameter inference 13
The coin-flipping problem 13
The general model 14
Choosing the likelihood 14
Choosing the prior 16
Getting the posterior 18
Computing and plotting the posterior 18
Influence of the prior and how to choose one 21
Communicating a Bayesian analysis 23
Model notation and visualization 23
Summarizing the posterior 24
Highest posterior density 24
Posterior predictive checks 27
Installing the necessary Python packages 28
Summary 29
Exercises 29
Chapter 2: Programming Probabilistically – A PyMC3 Primer 31
Probabilistic programming 32
Inference engines 33
Non-Markovian methods 33
Markovian methods 36

[i]
Table of Contents

PyMC3 introduction 46
Coin-flipping, the computational approach 46
Model specification 47
Pushing the inference button 48
Diagnosing the sampling process 48
Summarizing the posterior 55
Posterior-based decisions 55
ROPE 56
Loss functions 57
Summary 58
Keep reading 58
Exercises 59
Chapter 3: Juggling with Multi-Parametric and
Hierarchical Models 61
Nuisance parameters and marginalized distributions 62
Gaussians, Gaussians, Gaussians everywhere 64
Gaussian inferences 64
Robust inferences 69
Student's t-distribution 69
Comparing groups 75
The tips dataset 76
Cohen's d 80
Probability of superiority 81
Hierarchical models 81
Shrinkage 84
Summary 88
Keep reading 88
Exercises 89
Chapter 4: Understanding and Predicting Data with Linear
Regression Models 91
Simple linear regression 92
The machine learning connection 92
The core of linear regression models 93
Linear models and high autocorrelation 100
Modifying the data before running 101
Changing the sampling method 103
Interpreting and visualizing the posterior 103
Pearson correlation coefficient 107
Pearson coefficient from a multivariate Gaussian 110
Robust linear regression 113
Hierarchical linear regression 117
Correlation, causation, and the messiness of life 124
[ ii ]
 Table of Contents

Polynomial regression 126

Interpreting the parameters of a polynomial regression 129
Polynomial regression – the ultimate model? 130
Multiple linear regression 131
Confounding variables and redundant variables 135
Multicollinearity or when the correlation is too high 138
Masking effect variables 142
Adding interactions 144
The GLM module 145
Summary 146
Keep reading 146
Exercises 147
Chapter 5: Classifying Outcomes with Logistic Regression 149
Logistic regression 150
The logistic model 151
The iris dataset 152
The logistic model applied to the iris dataset 155
Making predictions 158
Multiple logistic regression 159
The boundary decision 159
Implementing the model 160
Dealing with correlated variables 162
Dealing with unbalanced classes 163
How do we solve this problem? 165
Interpreting the coefficients of a logistic regression 165
Generalized linear models 166
Softmax regression or multinomial logistic regression 167
Discriminative and generative models 171
Summary 174
Keep reading 174
Exercises 175
Chapter 6: Model Comparison 177
Occam's razor – simplicity and accuracy 178
Too many parameters leads to overfitting 179
Too few parameters leads to underfitting 181
The balance between simplicity and accuracy 182
Regularizing priors 183
Regularizing priors and hierarchical models 184
Predictive accuracy measures 185
Cross-validation 185

[ iii ]
Table of Contents

Information criteria 186

The log-likelihood and the deviance 186
Akaike information criterion 187
Deviance information criterion 188
Widely available information criterion 189
Pareto smoothed importance sampling leave-one-out cross-validation 190
Bayesian information criterion 190
Computing information criteria with PyMC3 190
A note on the reliability of WAIC and LOO computations 194
Interpreting and using information criteria measures 194
Posterior predictive checks 196
Bayes factors 197
Analogy with information criteria 199
Computing Bayes factors 199
Common problems computing Bayes factors 202
Bayes factors and information criteria 202
Summary 205
Keep reading 205
Exercises 205
Chapter 7: Mixture Models 207
Mixture models 207
How to build mixture models 209
Marginalized Gaussian mixture model 215
Mixture models and count data 216
The Poisson distribution 216
The Zero-Inflated Poisson model 218
Poisson regression and ZIP regression 220
Robust logistic regression 223
Model-based clustering 225
Fixed component clustering 227
Non-fixed component clustering 227
Continuous mixtures 228
Beta-binomial and negative binomial 228
The Student's t-distribution 229
Summary 230
Keep reading 230
Exercises 230
Chapter 8: Gaussian Processes 233
Non-parametric statistics 234
Kernel-based models 234
The Gaussian kernel 235
Kernelized linear regression 235

[ iv ]
 Table of Contents

Overfitting and priors 241

Gaussian processes 242
Building the covariance matrix 243
Sampling from a GP prior 243
Using a parameterized kernel 245
Making predictions from a GP 247
Implementing a GP using PyMC3 252
Posterior predictive checks 254
Periodic kernel 255
Summary 257
Keep reading 257
Exercises 258
Index 259

[v]
 Preface
Bayesian statistics has been around for more than 250 years now. During this time
it has enjoyed as much recognition and appreciation as disdain and contempt.
Through the last few decades it has gained more and more attention from people in
statistics and almost all other sciences, engineering, and even outside the walls of the
academic world. This revival has been possible due to theoretical and computational
developments. Modern Bayesian statistics is mostly computational statistics. The
necessity for flexible and transparent models and a more interpretation of statistical
analysis has only contributed to the trend.

Here, we will adopt a pragmatic approach to Bayesian statistics and we will not
care too much about other statistical paradigms and their relationship to Bayesian
statistics. The aim of this book is to learn about Bayesian data analysis with the help
of Python. Philosophical discussions are interesting but they have already been
undertaken elsewhere in a richer way than we can discuss in these pages.

We will take a modeling approach to statistics, we will learn to think in terms of

probabilistic models, and apply Bayes' theorem to derive the logical consequences
of our models and data. The approach will also be computational; models will
be coded using PyMC3—a great library for Bayesian statistics that hides most of
the mathematical details and computations from the user. Bayesian methods are
theoretically grounded in probability theory and hence it's no wonder that many
books about Bayesian statistics are full of mathematical formulas requiring a certain
level of mathematical sophistication. Learning the mathematical foundations of
statistics could certainly help you build better models and gain intuition about
problems, models, and results. Nevertheless, libraries, such as PyMC3 allow us to
learn and do Bayesian statistics with only a modest mathematical knowledge, as you
will be able to verify by yourself throughout this book.

[ vii ]
Preface

What this book covers

Chapter 1, Thinking Probabilistically – A Bayesian Inference Primer, tells us about
Bayes' theorem and its implications for data analysis. We then proceed to describe
the Bayesian-way of thinking and how and why probabilities are used to deal
with uncertainty. This chapter contains the foundational concepts used in the rest
of the book.

Chapter 2, Programming Probabilistically – A PyMC3 Primer, revisits the concepts from

the previous chapter, this time from a more computational perspective. The PyMC3
library is introduced and we learn how to use it to build probabilistic models, get
results by sampling from the posterior, diagnose whether the sampling was done
right, and analyze and interpret Bayesian results.

Chapter 3, Juggling with Multi-Parametric and Hierarchical Models, tells us about the
very basis of Bayesian modeling and we start adding complexity to the mix. We
learn how to build and analyze models with more than one parameter and how to
put structure into models, taking advantages of hierarchical models.

Chapter 4, Understanding and Predicting Data with Linear Regression Models, tells us
about how linear regression is a very widely used model per se and a building block
of more complex models. In this chapter, we apply linear models to solve regression
problems and how to adapt them to deal with outliers and multiple variables.

Chapter 5, Classifying Outcomes with Logistic Regression, generalizes the the linear
model from previous chapter to solve classification problems including problems
with multiple input and output variables.

Chapter 6, Model Comparison, discusses the difficulties associated with comparing

models that are common in statistics and machine learning. We will also learn a bit
of theory behind the information criteria and Bayes factors and how to use them to
compare models, including some caveats of these methods.

Chapter 7, Mixture Models, discusses how to mix simpler models to build more
complex ones. This leads us to new models and also to reinterpret models learned
in previous chapters. Problems, such as data clustering and dealing with count data,
are discussed.

Chapter 8, Gaussian Processes, closes the book by briefly discussing some more
advanced concepts related to non-parametric statistics. What kernels are, how to use
kernelized linear regression, and how to use Gaussian processes for regression are
the central themes of this chapter.

[ viii ]
 Preface

What you need for this book

This book is written for Python version >= 3.5, and it is recommended that you use
the most recent version of Python 3 that is currently available, although most of the
code examples may also run for older versions of Python, including Python 2.7 with
minor adjustments.

Maybe the easiest way to install Python and Python libraries is using Anaconda,
a scientific computing distribution. You can read more about Anaconda and
download it from https://www.continuum.io/downloads. Once Anaconda is in
our system, we can install new Python packages with this command: conda install
NamePackage.

We will use the following python packages:

• Ipython 5.0
• NumPy 1.11.1
• SciPy 0.18.1
• Pandas 0.18.1
• Matplotlib 1.5.3
• Seaborn 0.7.1
• PyMC3 3.0

Who this book is for

Undergraduate or graduate students, scientists, and data scientists who are not
familiar with the Bayesian statistical paradigm and wish to learn how to do Bayesian
data analysis. No previous knowledge of statistics is assumed, for either Bayesian or
other paradigms. The required mathematical knowledge is kept to a minimum and
all concepts are described and explained with code, figures, and text. Mathematical
formulas are used only when we think it can help the reader to better understand the
concepts. The book assumes you know how to program in Python. Familiarity with
scientific libraries such as NumPy, matplotlib, or Pandas is helpful but not essential.

[ ix ]
Preface

Conventions
In this book, you will find a number of text styles that distinguish between different
kinds of information. Here are some examples of these styles and an explanation of
their meaning.

Code words in text, database table names, folder names, filenames, file extensions,
pathnames, dummy URLs, user input, and Twitter handles are shown as follows: "To
compute the HPD in the correct way we will use the function plot_post."

A block of code is set as follows:

n_params = [1, 2, 4]
p_params = [0.25, 0.5, 0.75]
x = np.arange(0, max(n_params)+1)
f, ax = plt.subplots(len(n_params), len(p_params), sharex=True,
sharey=True)
for i in range(3):
for j in range(3):
n = n_params[i]
p = p_params[j]
y = stats.binom(n=n, p=p).pmf(x)
ax[i,j].vlines(x, 0, y, colors='b', lw=5)
ax[i,j].set_ylim(0, 1)
ax[i,j].plot(0, 0, label="n = {:3.2f}\np =
{:3.2f}".format(n, p), alpha=0)
ax[i,j].legend(fontsize=12)
ax[2,1].set_xlabel('$\\theta$', fontsize=14)
ax[1,0].set_ylabel('$p(y|\\theta)$', fontsize=14)
ax[0,0].set_xticks(x)

Any command-line input or output is written as follows:

conda install NamePackage

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[x]
 Preface

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[ xi ]
Preface

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[ xii ]
 Thinking Probabilistically -
A Bayesian Inference Primer
Probability theory is nothing but common sense reduced to calculation.

-Pierre-Simon Laplace

In this chapter, we will learn the core concepts of Bayesian statistics and some of the
instruments in the Bayesian toolbox. We will use some Python code in this chapter,
but this chapter will be mostly theoretical; most of the concepts in this chapter will be
revisited many times through the rest of the book. This chapter, being intense on the
theoretical side, may be a little anxiogenic for the coder in you, but I think it will ease
the path to effectively applying Bayesian statistics to your problems.

In this chapter, we will cover the following topics:

• Statistical modeling
• Probabilities and uncertainty
• Bayes' theorem and statistical inference
• Single parameter inference and the classic coin-flip problem
• Choosing priors and why people often don't like them, but should
• Communicating a Bayesian analysis
• Installing all Python packages

[1]
Thinking Probabilistically - A Bayesian Inference Primer

Statistics as a form of modeling

Statistics is about collecting, organizing, analyzing, and interpreting data, and
hence statistical knowledge is essential for data analysis. Another useful skill when
analyzing data is knowing how to write code in a programming language such as
Python. Manipulating data is usually necessary given that we live in a messy world
with even messier data, and coding helps to get things done. Even if your data is
clean and tidy, programming will still be very useful since modern Bayesian statistics
is mostly computational statistics.

Most introductory statistical courses, at least for non-statisticians, are taught as a

collection of recipes that more or less go like this; go to the the statistical pantry, pick
one can and open it, add data to taste and stir until obtaining a consistent p-value,
preferably under 0.05 (if you don't know what a p-value is, don't worry; we will
not use them in this book). The main goal in this type of course is to teach you how
to pick the proper can. We will take a different approach: we will also learn some
recipes, but this will be home-made rather than canned food; we will learn how to
mix fresh ingredients that will suit different gastronomic occasions. But before we
can cook, we must learn some statistical vocabulary and also some concepts.

Exploratory data analysis

Data is an essential ingredient of statistics. Data comes from several sources, such as
experiments, computer simulations, surveys, field observations, and so on. If we are
the ones that will be generating or gathering the data, it is always a good idea to first
think carefully about the questions we want to answer and which methods we will
use, and only then proceed to get the data. In fact, there is a whole branch of statistics
dealing with data collection known as experimental design. In the era of data deluge,
we can sometimes forget that gathering data is not always cheap. For example, while
it is true that the Large Hadron Collider (LHC) produces hundreds of terabytes a
day, its construction took years of manual and intellectual effort. In this book we will
assume that we already have collected the data and also that the data is clean and
tidy, something rarely true in the real world. We will make these assumptions in
order to focus on the subject of this book. If you want to learn how to use Python for
cleaning and manipulating data and also a primer on machine learning, you should
probably read the book Python Data Science Handbook by Jake VanderPlas.

[2]
 Chapter 1

OK, so let's assume we have our dataset; usually, a good idea is to explore and
visualize it in order to get some intuition about what we have in our hands. This can
be achieved through what is known as Exploratory Data Analysis (EDA), which
basically consists of the following:

• Descriptive statistics
• Data visualization

The first one, descriptive statistics, is about how to use some measures (or statistics)
to summarize or characterize the data in a quantitative manner. You probably
already know that you can describe data using the mean, mode, standard deviation,
interquartile ranges, and so forth. The second one, data visualization, is about
visually inspecting the data; you probably are familiar with representations such
as histograms, scatter plots, and others. While EDA was originally thought of as
something you apply to data before doing any complex analysis or even as an
alternative to complex model-based analysis, through the book we will learn that
EDA is also applicable to understanding, interpreting, checking, summarizing, and
communicating the results of Bayesian analysis.

Inferential statistics
Sometimes, plotting our data and computing simple numbers, such as the average
of our data, is all we need. Other times, we want to make a generalization based
on our data. We may want to understand the underlying mechanism that could
have generated the data, or maybe we want to make predictions for future
(yet unobserved) data points, or we need to choose among several competing
explanations for the same observations. That's the job of inferential statistics. To do
inferential statistics we will rely on probabilistic models. There are many types of
models and most of science, and I will add all of our understanding of the real world,
is through models. The brain is just a machine that models reality (whatever reality
might be) see this TED talk about the machine that builds the reality http://www.
tedxriodelaplata.org/videos/m%C3%A1quina-construye-realidad.

[3]
Thinking Probabilistically - A Bayesian Inference Primer

What are models? Models are simplified descriptions of a given system (or process).
Those descriptions are purposely designed to capture only the most relevant aspects
of the system, and hence, most models do not pretend they are able to explain
everything; on the contrary, if we have a simple and a complex model and both
models explain the data more or less equally well, we will generally prefer the
simpler one. This heuristic for simple models is known as Occam's razor, and we will
discuss how it is related to Bayesian analysis in Chapter 6, Model Comparison.

Model building, no matter which type of model you are building, is an iterative
process following more or less the same basic rules. We can summarize the Bayesian
modeling process using three steps:

1. Given some data and some assumptions on how this data could have been
generated, we will build models. Most of the time, models will be crude
approximations, but most of the time this is all we need.
2. Then we will use Bayes' theorem to add data to our models and derive the
logical consequences of mixing the data and our assumptions. We say we are
conditioning the model on our data.
3. Lastly, we will check that the model makes sense according to different
criteria, including our data and our expertise on the subject we are studying.

In general, we will find ourselves performing these three steps in a non-linear

iterative fashion. Sometimes we will retrace our steps at any given point: maybe we
made a silly programming mistake, maybe we found a way to change the model and
improve it, maybe we need to add more data.

Bayesian models are also known as probabilistic models because they are built
using probabilities. Why probabilities? Because probabilities are the correct
mathematical tool to model the uncertainty in our data, so let's take a walk through
the garden of forking paths.

[4]
 Chapter 1

Probabilities and uncertainty

While Probability Theory is a mature and well-established branch of mathematics,
there is more than one interpretation of what probabilities are. To a Bayesian, a
probability is a measure that quantifies the uncertainty level of a statement. If we
know nothing about coins and we do not have any data about coin tosses, it is
reasonable to think that the probability of a coin landing heads could take any value
between 0 and 1; that is, in the absence of information, all values are equally likely,
our uncertainty is maximum. If we know instead that coins tend to be balanced, then
we may say that the probability of a coin landing is exactly 0.5 or may be around 0.5
if we admit that the balance is not perfect. If now, we collect data, we can update
these prior assumptions and hopefully reduce the uncertainty about the bias of the
coin. Under this definition of probability, it is totally valid and natural to ask about
the probability of life on Mars, the probability of the mass of the electron being 9.1 x
10-31 kg, or the probability of the 9th of July of 1816 being a sunny day. Notice, for
example, that the question of whether or not life exists on Mars has a binary outcome
but what we are really asking is how likely is it to find life on Mars given our data
and what we know about biology and the physical conditions on that planet? The
statement is about our state of knowledge and not, directly, about a property of
nature. We are using probabilities because we cannot be sure about the events,
not because the events are necessarily random. Since this definition of probability
is about our epistemic state of mind, sometimes it is referred to as the subjective
definition of probability, explaining the slogan of subjective statistics often attached
to the Bayesian paradigm. Nevertheless, this definition does not mean all statements
should be treated as equally valid and so anything goes; this definition is about
acknowledging that our understanding about the world is imperfect and conditioned
on the data and models we have made. There is not such a thing as a model-free or
theory-free understanding of the world; even if it were be possible to free ourselves
from our social preconditioning, we will end up with a biological limitation: our
brain, subject to the evolutionary process, has been wired with models of the world.
We are doomed to think like humans and we will never think like bats or anything
else! Moreover, the universe is an uncertain place and, in general the best we can
do is to make probabilistic statements about it. Notice that it does not matter if
the underlying reality of the world is deterministic or stochastic; we are using
probability as a tool to quantify uncertainty.

[5]
Thinking Probabilistically - A Bayesian Inference Primer

Logic is about thinking without making mistakes. Under the Aristotelian or classical
logic, we can only have statements taking the values true or false. Under the
Bayesian definition of probability, certainty is just a special case: a true statement has
a probability of 1, a false one has probability 0. We would assign a probability of 1
about life on Mars only after having conclusive data indicating something is growing
and reproducing and doing other activities we associate with living organisms.
Notice, however, that assigning a probability of 0 is harder because we can always
think that there is some Martian spot that is unexplored, or that we have made
mistakes with some experiment, or several other reasons that could lead us to falsely
believe life is absent on Mars when it is not. Related to this point is Cromwell's rule,
stating that we should reserve the use of the prior probabilities of 0 or 1 to logically
true or false statements. Interesting enough, Cox mathematically proved that if we
want to extend logic to include uncertainty we must use probabilities and probability
theory. Bayes' theorem is just a logical consequence of the rules of probability as
we will see soon. Hence, another way of thinking about Bayesian statistics is as an
extension of logic when dealing with uncertainty, something that clearly has nothing
to do with subjective reasoning in the pejorative sense. Now that we know the
Bayesian interpretation of probability, let's see some of the mathematical properties
of probabilities. For a more detailed study of probability theory, you can read
Introduction to probability by Joseph K Blitzstein & Jessica Hwang.

Probabilities are numbers in the interval [0, 1], that is, numbers between 0 and 1,
including both extremes. Probabilities follow some rules; one of these rules is the
product rule:

p ( A, B ) = p ( A | B ) p ( B )

We read this as follows: the probability of A and B is equal to the probability of

A given B, times the probability of B. The expression p(A, B) represents the joint
probability of A and B. The expression p(A|B) is used to indicate a conditional
probability; the name refers to the fact that the probability of A is conditioned on
knowing B. For example, the probability that a pavement is wet is different from
the probability that the pavement is wet if we know (or given that) is raining. A
conditional probability can be larger than, smaller than or equal to the unconditioned
probability. If knowing B does not provides us with information about A, then
p(A|B)=p(A). That is A and B are independent of each other. On the contrary, if
knowing B gives us useful information about A, then the conditional probability
could be larger or smaller than the unconditional probability depending on whether
knowing B makes A less or more likely.

[6]
Exploring the Variety of Random
Documents with Different Content
The Project Gutenberg eBook of Woman in
Prison
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Title: Woman in Prison

Author: Caroline H. Woods

Release date: November 24, 2013 [eBook #44273]

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Language: English

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*** START OF THE PROJECT GUTENBERG EBOOK WOMAN IN

PRISON ***
 WOMAN IN PRISON.
BY

CAROLINE H. WOODS.

NEW YORK:

PUBLISHED BY HURD AND HOUGHTON.

Cambridge: Riverside Press.

1869.

Entered according to Act of Congress, in the year 1869, by

Caroline H. Woods,
in the Clerk's Office of the District Court for the District of Massachusetts.
RIVERSIDE, CAMBRIDGE:
STEREOTYPED AND PRINTED BY
H. O. HOUGHTON AND COMPANY.
 WHY WRITTEN.
I was reading an evening paper. I glanced over the advertisements.
One attracted my attention, and held it so strongly that I read it over
and over, again and again. There was nothing unusual in it to
ordinary observation. It read, "Wanted.—At the Penitentiary, a
Matron. Inquire at the Institution."
I turned the paper over to read the general news; but could not
place my thoughts so as to comprehend the meaning of the words
before my sight. Without the intention to do so, I looked again at
the advertisement. It became a study to me.
Said Thought—If you were to answer that advertisement, and
obtain the situation, it would place you upon missionary ground, and
at the same time give you employment which would afford you a
support while you are teaching the ignorant. You would get
knowledge in the position. A new phase of life would be opened to
your view. You would have an opportunity to observe, practically,
how well the present system of prison discipline is adapted to reform
convicts, and repress crime. But the cost is too much. I cannot
become a Matron in a Penitentiary.
I laid the paper down, without reading it, because I could see
nothing in it except that advertisement.
The next day I went in town, sat down in the office of a friend, and
took up a morning paper. No sooner had I opened it than that
advertisement spread itself out before me. It changed the form of its
appeal; left out what my selfishness might gain, to enlist my
compassion and aid, entirely, in what I might accomplish for others.
It called to me, in piteous tones, to go work for the prisoner. It was
the echo of a voice that I long ago heard, Come into our prisons,
and help us, we beseech you!
I cannot! I have other things to do, and they are as much for the
benefit of humanity as anything I may be able to accomplish for you.
My spirit darkened as I made the answer; a cloud of guilt settled
down upon it. I threw down the paper in order to dissipate it, and to
avoid the plea.
I turned and talked with my friend; but my thoughts were not in
what we were saying. That advertisement followed them, and filled
them to the exclusion of every other subject.
In the abstraction which it caused the hour in which I was to leave
the city passed, and I missed my train. I must remain and avail
myself of another.
While I was waiting, that advertisement returned to my reflections,
and urged its cause imperatively as a command. It was a call, to me,
resistless as the voice that awoke the young Israelitish Prophet from
his slumbers. In another moment the struggle with my pride was
over, and my spirit answered,—I will go, even to lust-besotted
Sodom if thou leadest, Light of my path!
I seated myself in a street car, went to the prison, applied for the
place, and obtained it.
Day by day I wrote down what I saw and heard, what I said and
did. Why? In obedience to the same Voice that called me to the
work.
The tale is before you.
May it touch the heart of every one who reads the story, and melt it
into a compassion which will labor for the redemption of the
prisoner; into a pity which will echo around the cry—Open the prison
doors, not to let the prisoner go free, but to let in, to him, the light
of moral knowledge, and the discipline of Christian charity.
 CONTENTS.
PAGE

WHY WRITTEN iii

I. FIRST DAY IN PRISON 1

II. AT NIGHT 13

III. SECOND DAY IN PRISON 23

IV. A QUARREL, AND DISCIPLINE 34

V. THE SUPERVISOR, AND THE RULES 48

VI. FIRST NIGHT ALONE IN PRISON 58

VII. THE MASTER AND THE RULES 75

VIII. MRS. HARDHACK 79

IX. A BREAD-AND-WATER BOARDER 87

X. AN ARRIVAL 93

XI. INSIDE MANAGEMENT 98

XII. SUNDAY 102

XIII. LIFE AMONG THE LOWLY 110

XIV. INSPECTION OF PRIVATE APARTMENTS 127

XV. A DAY OF ODDS AND ENDS 138

 XVI. A FRIGHT 151

XVII. VISITING DAY 156

XVIII. CALLAHAN AGAIN 163

XIX. DISCOMFORTS, AND THE END 178

 I.
FIRST DAY IN PRISON.

It was Saturday morning that I became an inmate of the

Penitentiary.
I was conducted to the kitchen, where I was to oversee the cooking
for the prisoners, and to the prison adjoining it, which I was to see
kept in order, by the Deputy Master of the institution, who gave me
my keys and installed me in my office of Prison Matron.
When we first went in he called the six women who do the work in
the kitchen, and the three "sweeps" who keep the prison clean, to
him, and presented their new mistress, in my person, to them.
They were convicts that surrounded me at his call; but they were
human beings. Human faces looked up to mine for sympathy and
care. Some of them were fine looking, even in their coarse uniform,
some were pretty as I picked them out one by one. They all looked
at me earnestly, for a few moments, as though they were reading
their sentence of harshness or kindly treatment, under my rule, in
my face; then, turned away to their work again.
They whispered as they stood together, and I saw by their furtive
glances that they were watching, and discussing me, as I walked
around to take a survey of my new field of labor. They were
undoubtedly commenting upon my personal appearance; and
making their predictions as to my sharpness in detecting their
impositions, and ability to control their perverseness; or, I imagined
so.
 The Deputy showed me the mush boiler, that would cook two large
tubs full of that farinaceous edible at a time; the potato steamer,
that would hold four barrels of that esculent vegetable at a cooking;
the soup and coffee kettles, of still larger dimensions; and that
comprised all of the apparatus required in preparing the mammoth
meals which were to serve above four hundred people. These
cooking utensils were kept in operation by pipes conducting steam
to them from a boiler stationed in the middle of the room.
When he put the steam boiler under my direction I shrank back in
terror from the task of managing it. The huge culinary apparatus,
which he had been exhibiting, although outside the pale of ordinary
housekeeping, was still within the reach of my understanding; but I
had no idea of the management of steam; it was not only a difficult,
but dangerous affair.
"The house will surely be blown up if you leave the care of that
upon me," I said to him.
"You must watch it very closely."
"I don't know how, and I have no aptness for learning that kind of
science."
"One of the women will tend it." And he went on with explanations
that were all Greek to me. "It is safe when you have on twenty
pounds of steam. There is your gauge," and he pointed to a clock-
like looking affair on the wall. "That hand will move round and tell
you how much steam you have on. You must keep water enough in
the boiler or you will get blown up. If it runs from that centre
stopcock, on the side, it is safe. You notice that glass tube in front.
The water is just as high in that as it is in the boiler. This faucet is to
let the water off if you get the boiler too full. Turn that faucet when
you let the water on," and he went along and pointed to one in a
pipe by the wall, "and that pump is there in case of accident. You
must have it worked every day so as to keep it in order."
 All knowledge is useful, I thought, and in time I shall understand
running a steam-engine. As the women have been trusted with the
dangerous thing, they may still continue to be, till I have leisure to
learn the science of steam as applied to cooking.
After I had taken a survey of the kitchen the Deputy took me into
the women's prison which led out of it.
The centre of the hollow square, in which the dormitories are built,
looked like a huge block of glittering ice, so white were the washed
walls of brick and stone. The black, grated doors of the cells,
inserted into them, like the teeth of grinning demons, were ranged
along the sides about two feet apart, tier after tier, five stories, one
above another.
The Deputy led me along past the iron doors. I trembled and
shrank back; but I had no idea of receding from my undertaking. I
"screwed my courage to the sticking-point," and looked into the
narrow, stone rooms; but it was many days before I could force
myself to enter one.
I grew heart-sick, and faint with apprehension of unknown terrors
at their cheerless aspect.
"What lodgings for human beings!" I exclaimed.
"They are not very pleasant," said the Deputy.
"If you were the one to blame for it I should certainly charge you
with great inhumanity."
"I suppose you will think us very cruel sometimes."
"In this case I don't know as you can help it. You did not make
these sleeping apartments for the prisoners. The public functionaries
of the State may be thanked for showing such tender mercies as
these."
 "We are used to seeing them, and they don't look to us as they do
to you."
"Does that make them any more comfortable for the prisoners? Do
they get used to them so as to be comfortable?"
"I presume so. I know they are more comfortable places than some
had before they came here."
"Then it should be the work of the vaunting Christianity of this
religious land to raise such degradation to cleanliness, comfort, and
respectability."
"There might be a great deal done in that direction if people were
only disposed to do it."
"Our prisons are rather private affairs, I believe. They can only be
visited on certain days and occasions."
"It would be very inconvenient for our work to have people running
in, and over the place at all times. We could not have it. And it
wouldn't be liked by the prisoners to be gazed at constantly."
I made no reply; but I thought it might have a salutary effect upon
the discipline of the prison, which he had just said I might think
cruel, to be exposed to the observation of the public. The prisoners
must have lost the sensibility which would shrink from being made a
spectacle before they came in there. If visiting were allowed only on
certain days and occasions, the place and the convicts would be put
in order for company, and a very incorrect idea of the every-day life
of the prisoners would be obtained.
If there were liberty to visit the place, every day, many might go
from curiosity, and it might become annoying. That very curiosity
might discover and discuss faults in the management, which ought
to be remedied, and thus produce a counterbalancing benefit.
The officers might dislike such scrutiny, especially, if they were not
doing their duty. They are officers of the government. Is it not
proper that their conduct should be looked after by the people as
much as that of any other government official?
Evil comrades might go in and hold improper communication with
the prisoners. Can they not do that on regular visiting days?
Is it not only the work of humanity to see that crime is punished in
a way that will not increase it; but also that of the legislator as a
matter of civil policy; and that of the taxpayer as a matter of
personal interest. It should interest every man and woman as a
matter of personal protection from the depredations of vice to know
how convicts are treated, and to judge whether that treatment tends
to reform the criminal, or to harden and lead him deeper into crime
when he is let out into the world again to pursue his own ways.
Ought the punishment of criminals, who have been tried, convicted,
and sentenced publicly, to be conducted in secret? It is to be
presumed that the keeper of the prison is trusty. There should be no
presumption in the matter. It should be known that he is so, and he
should be kept so by the ceaseless vigilance of public inspection.
What is the quarterly, or semi-annual visit of fifty or a hundred men
when the visit has been notified, and the prison put in order for their
reception, towards effecting that?
My residence in that prison led me to see that the descriptions of
Dickens, and his compeers in the regions of fictitious writing, have
given, not the poetic illusions of imaginary sufferings to the
contemplation of the world—hardly a vivid picture of the truth.
God speed the day when our prisons and penitentiaries may take a
place beside public schools, orphan asylums, houses of refuge, all
institutions for the cultivation of a knowledge which tends to the
elevation of virtue, and the suppression of vice, in the care of the
public!
Our own children may not stimulate to an interest in them. Our
own children may not require the benefit of the public school, or
orphan asylum; but somebody's children will. In working for the
elevation of everybody's children are we not benefiting our own?
After he had shown me around, so that I might take a general
survey of my field of labor, the Deputy left me with my charge,
saying,—
"You are mistress here. No one has a right to interfere with you,
and you are responsible to no one but me, or the Master."
"But the Head Matron will, of course, come and instruct me in the
details of my work. I must know what work belongs to each woman,
and how she is expected to perform it."
"The women know their work and will do it. The most you have to
do is to keep order."
"That may be a man's idea of managing a kitchen; but there are a
great many details that I ought to understand in order to get the
work properly done, and done in its proper time; and with the
greatest ease to myself and the women."
"The other Matrons will tell you. I will tell you all I can."
I thought, but I did not say it,—You are better disposed than
informed. He saw by the anxious expression of my face that I was
not satisfied, and added, "The women know, they will tell you."
I made no reply; but I thought—It is not the proper thing for me to
receive my instructions from the convicts. It is their place to be
instructed by me. If I am taught by them, I am placed in an inferior
position to them. In order to entertain a proper respect for me they
should look up to me as their superior in all things.
The arrangement for receiving my directions from them placed me
too much in their power also. It would be only indulging natural
proclivities to "play off" on me under the circumstances; and I could
hardly expect these poor, abandoned creatures to be superior to the
temptation to do it when the opportunity was afforded them.
 I could not consider such teachers reliable. If, by misleading me,
with regard to a rule of the institution, they could obtain an
indulgence, or relieve themselves of a burden, would they not take
the advantage which they had of me and do it. I was suspicious that
they would.
There was, probably, some pride mixed with these considerations,
that rebelled against becoming a pupil of convicts when I was their
mistress.
I stood looking on, or walking around, watching the movements of
the women very narrowly, till one of the other Matrons came in.
Then, I went to her with a volume of questions.
To most of them I received the answer,—
"I don't know about that particularly. I have never had anything to
do with this department."
"Then, how am I to learn my duties, and get definite orders for the
regulation of my work? Is there no Head Matron, no superior officer
in the women's prison to whom I can go?"
"The Master's wife is enrolled as Head Matron, and receives pay as
such, but she never comes round."
"I would go to her if I knew where to find her."
"I don't think she knows much more about it than you do, if you
were to go to her. We will all tell you."
"But you don't know. If there is a Head Matron, and she is paid for
doing the duties of one, why does she not perform them? Is she
enrolled head officer of this prison merely to obtain the salary? The
government is very obliging to make her office a sinecure."
I was already perplexed—I was beginning to get vexed.
"Her husband does them for her, perhaps."
 "Perhaps! Then why is he not here, to tell me the work which
belongs to each woman, and how she is to do it; what work is
required, and how I am to get my things to do with? But how can
the Master attend to his own duties and those of the Head Matron
too?"
"The Deputy will tell you."
"He must have his own duties to attend to—how can he perform
hers? He is just as willing to tell me as you are, and I don't think he
knows any more about my place than you do."
"The women know, they will tell you."
I was thrown back upon the convicts again for my instructions.
I went on, despairing of help, to study them out as best I could.
Sometimes by asking left-hand questions of the women, and
sometimes by getting direct explanations from them; but chiefly by
watching the progress of the work. The place seemed to me full of
disorder, confusion, and dirt.
When the Deputy came round again, I was full of trouble.
He said, when I complained to him,—
"You will find things in confusion. The Matron who went away
yesterday was inefficient."
"Perhaps so," I replied; "but the confusion appears to me to date
farther back than the last Matron. It arises from the want of a head
officer to regulate affairs."
"I have double the trouble on this side, with four Matrons and a
hundred women, than with three hundred men and more than a
dozen officers on the other."
"You would insinuate that women are more difficult to get on with
than men. I make a very different solution of the difficulty in this
particular case. You are on the ground all of the time; explain his
duty to every officer, and see that he does it. That makes the
officer's work distinct before him. It is done under your eye, which
makes it promptly and well done. If that were the case on this side,
we might be as orderly, and have as little trouble in performing our
part, as you on yours. The cook tells me that certain work belongs to
the slide woman; the slide woman says it belongs to the sink
women; the sink women shift it on the steam woman, and so I am
kept on the chase, from one to another, for some one to do a piece
of labor. I do not know who ought to do it, and they know it. If they
do not intend to confuse me, they intend to clear themselves of all
the work they can."
"Use your own judgment, and call on whom you please. They are
all obliged to obey any order that you give."
"If I call upon one to do the work that has formerly been done by
another, I stir up ill feelings among the prisoners towards each other,
and contention, and they think me hard and unjust. It makes me
trouble. They obey my order reluctantly, and say, 'That isn't my
work.'"
"If they quarrel, they know the punishment. If they refuse to obey
your orders, report them to me, and I will put them where they will
be glad to obey." He nodded towards the prison door.
I knew he must refer to some kind of punishment. I did not know
what; but frightful visions of the cruelties of which I had read rose in
my imagination, and I said no more.
I vowed to myself that I would never get them punished by
refusing to obey my unjust exactions if I could help it.
My thoughts did not stop with my words. I reasoned with myself. If
my ignorance, or bad management, cause me to be unjust towards
those women, and if I, by my injustice, arouse their bad temper so
as to cause them to be punished, who will be most in fault? I
decided that I should be. The question suggested itself to me—If
you get them punished unjustly who will avenge them? The All-
seeing-Eye will notice, and avenge it. I will be careful.
I resolved to feel my way along softly and carefully. There was no
relief for my dilemma, except in my own ingenuity to find out the
ways of the place, and the proper management to apply to it.
 II.
AT NIGHT.

At seven o'clock, P. M., came the marching in to supper, and the

locking up of all the prisoners.
I looked to see, as they filed past me, one by one, if they carried
marks of their crimes upon their faces. I saw nothing unusual in the
mass; occasionally an individual countenance betrayed the vicious
habits which had brought the woman there. If I had not known that
they were convicts, I should never have suspected them to be
different from the ordinary poor people who are constantly passing
along the streets.
About sixty of the women in the Penitentiary were employed in the
shop upon contract vests, pantaloons, coats, and shirts. There were
about fifty employed upon sewing-machines. The rest cut, basted,
and finished the work.
There were from four to ten in the wash-room. These were all
lodged in my domain, with the exception of two or three who slept
in the hospital.
When they left their work, at night, they were placed in file, in the
order of their cells, and marched into the prison past the ration door,
where their meals were handed out to them, through a slide, from
the kitchen.
Their supper was a "skillet pan" of mush, or a slice of bread, and a
quart of rye coffee, which was taken to their cells to be eaten after
they were locked in their rooms—or stone dens, I called them in my
indignation. The sight of those little, cramped stone cells recalled to
my memory the pictures of dungeons, and imprisonments, and
tortures which I had looked at in my childhood till my heart was
racked with agony at the cruelties which they portrayed.
It was no paper picture that I was looking upon, but a stern reality;
and my shrinking spirit asked again and again, as I saw those poor
creatures marched in, and immured for the night,—Why did your
folly prompt you to undertake such work?
Never shall I forget the hissing creak of the sliding bar as it closed
them in; or the click of the lock as I turned the key in it, for the first
time, upon those poor wretches. Long before I got through with the
thirty-six locks, it fell to my share to bolt, my fingers were bruised,
and my arm ached; but not so much as my heart.
I looked in upon the poor things, one by one, as I locked them in.
An agony of pity worked itself into my soul, and oppressed me
almost to suffocation.
I said to myself—Is this a woman's work? May be. If it must be
done, it should be done tenderly. Great God, for Christ's sake, pity
them in their cold, damp, narrow cells, and make their straw pallets
couches of rest! I prayed mentally as I left the grated doors.
I had thought this to be missionary ground. I might teach some of
them the way to Eternal Life, and the way to reformation. Alas! I
found little chance with those who went to the shop and wash-room.
They rose at sunrise, and worked till sunset. No one was allowed to
hold communication with them, but their own Overseer, about their
work. Neither were they allowed to talk in their cells at night, and
they would have been too tired if they had been given the liberty to
do so. The taskmaster had been over them all day to drive them,
pitilessly, to fulfill their sentence of so many months hard labor in
the Penitentiary.
I turned away, sadly, from that disappointed hope; but I saw the
opportunity still before me to teach the nine, whom I had under my
immediate care, to govern their tempers, and their passions, and to
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